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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        About MultiQC

        This report was generated using MultiQC, version 1.33

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        MultiQC is developed by Seqera.

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        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the bigbio/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.
        Report generated on 2026-01-21, 09:00 UTC based on data in: /home/runner/work/pmultiqc/pmultiqc/data_temp
        Because this report contains a lot of samples, you may need to click 'Show plot' to see some graphs.

        pmultiqc

        pmultiqc is a MultiQC module to show the pipeline performance of mass spectrometry based quantification pipelines such as nf-core/quantms, MaxQuant, DIA-NN, and FragPipe.https://github.com/bigbio/pmultiqc

        Experimental Design and Metadata

        Experimental Design

        This table shows the design of the experiment. I.e., which files and channels correspond to which sample/condition/fraction.
        You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html
        Showing 160/160 rows and 5/5 columns.
        Sample NameMSstats ConditionMSstats BioReplicateFraction GroupFractionLabel
         
        Sample 1
        blood plasma1
         
         ↳ FP-1A1
        111
         
        Sample 2
        blood plasma2
         
         ↳ FP-1A2
        211
         
        Sample 3
        blood plasma3
         
         ↳ FP-1A3
        311
         
        Sample 4
        blood plasma4
         
         ↳ FP-1A4
        411
         
        Sample 5
        blood plasma5
         
         ↳ FP-1B1
        511
         
        Sample 6
        blood plasma6
         
         ↳ FP-1B2
        611
         
        Sample 7
        blood plasma7
         
         ↳ FP-1B3
        711
         
        Sample 8
        blood plasma8
         
         ↳ FP-1B4
        811
         
        Sample 9
        blood plasma9
         
         ↳ FP-1C1
        911
         
        Sample 10
        blood plasma10
         
         ↳ FP-1C2
        1011
         
        Sample 11
        blood plasma11
         
         ↳ FP-1C3
        1111
         
        Sample 12
        blood plasma12
         
         ↳ FP-1C4
        1211
         
        Sample 13
        blood plasma13
         
         ↳ FP-1D1
        1311
         
        Sample 14
        blood plasma14
         
         ↳ FP-1D2
        1411
         
        Sample 15
        blood plasma15
         
         ↳ FP-1D3
        1511
         
        Sample 16
        blood plasma16
         
         ↳ FP-1D4
        1611
         
        Sample 17
        blood plasma17
         
         ↳ FP-1E1
        1711
         
        Sample 18
        blood plasma18
         
         ↳ FP-1E2
        1811
         
        Sample 19
        blood plasma19
         
         ↳ FP-1E3
        1911
         
        Sample 20
        blood plasma20
         
         ↳ FP-1E4
        2011
         
        Sample 21
        blood plasma21
         
         ↳ FP-2A1
        2111
         
        Sample 22
        blood plasma22
         
         ↳ FP-2A2
        2211
         
        Sample 23
        blood plasma23
         
         ↳ FP-2A3
        2311
         
        Sample 24
        blood plasma24
         
         ↳ FP-2A4
        2411
         
        Sample 25
        blood plasma25
         
         ↳ FP-2B1
        2511
         
        Sample 26
        blood plasma26
         
         ↳ FP-2B2
        2611
         
        Sample 27
        blood plasma27
         
         ↳ FP-2B3
        2711
         
        Sample 28
        blood plasma28
         
         ↳ FP-2B4
        2811
         
        Sample 29
        blood plasma29
         
         ↳ FP-2C1
        2911
         
        Sample 30
        blood plasma30
         
         ↳ FP-2C2
        3011
         
        Sample 31
        blood plasma31
         
         ↳ FP-2C3
        3111
         
        Sample 32
        blood plasma32
         
         ↳ FP-2C4
        3211
         
        Sample 33
        blood plasma33
         
         ↳ FP-2D1
        3311
         
        Sample 34
        blood plasma34
         
         ↳ FP-2D2
        3411
         
        Sample 35
        blood plasma35
         
         ↳ FP-2D3
        3511
         
        Sample 36
        blood plasma36
         
         ↳ FP-2D4
        3611
         
        Sample 37
        blood plasma37
         
         ↳ FP-2E1
        3711
         
        Sample 38
        blood plasma38
         
         ↳ FP-2E2
        3811
         
        Sample 39
        blood plasma39
         
         ↳ FP-2E3
        3911
         
        Sample 40
        blood plasma40
         
         ↳ FP-2E4
        4011
         
        Sample 41
        blood plasma41
         
         ↳ FP-3A1
        4111
         
        Sample 42
        blood plasma42
         
         ↳ FP-3A2
        4211
         
        Sample 43
        blood plasma43
         
         ↳ FP-3A3
        4311
         
        Sample 44
        blood plasma44
         
         ↳ FP-3A4
        4411
         
        Sample 45
        blood plasma45
         
         ↳ FP-3B1
        4511
         
        Sample 46
        blood plasma46
         
         ↳ FP-3B2
        4611
         
        Sample 47
        blood plasma47
         
         ↳ FP-3B3
        4711
         
        Sample 48
        blood plasma48
         
         ↳ FP-3B4
        4811
         
        Sample 49
        blood plasma49
         
         ↳ FP-3C1
        4911
         
        Sample 50
        blood plasma50
         
         ↳ FP-3C2
        5011
         
        Sample 51
        blood plasma51
         
         ↳ FP-3C3
        5111
         
        Sample 52
        blood plasma52
         
         ↳ FP-3C4
        5211
         
        Sample 53
        blood plasma53
         
         ↳ FP-3D1
        5311
         
        Sample 54
        blood plasma54
         
         ↳ FP-3D2
        5411
         
        Sample 55
        blood plasma55
         
         ↳ FP-3D3
        5511
         
        Sample 56
        blood plasma56
         
         ↳ FP-3D4
        5611
         
        Sample 57
        blood plasma57
         
         ↳ FP-3E1
        5711
         
        Sample 58
        blood plasma58
         
         ↳ FP-3E2
        5811
         
        Sample 59
        blood plasma59
         
         ↳ FP-3E3
        5911
         
        Sample 60
        blood plasma60
         
         ↳ FP-3E4
        6011
         
        Sample 61
        blood plasma61
         
         ↳ FP-4A1
        6111
         
        Sample 62
        blood plasma62
         
         ↳ FP-4A2
        6211
         
        Sample 63
        blood plasma63
         
         ↳ FP-4A3
        6311
         
        Sample 64
        blood plasma64
         
         ↳ FP-4A4
        6411
         
        Sample 65
        blood plasma65
         
         ↳ FP-4B1
        6511
         
        Sample 66
        blood plasma66
         
         ↳ FP-4B2
        6611
         
        Sample 67
        blood plasma67
         
         ↳ FP-4B3
        6711
         
        Sample 68
        blood plasma68
         
         ↳ FP-4B4
        6811
         
        Sample 69
        blood plasma69
         
         ↳ FP-4C1
        6911
         
        Sample 70
        blood plasma70
         
         ↳ FP-4C2
        7011
         
        Sample 71
        blood plasma71
         
         ↳ FP-4C3
        7111
         
        Sample 72
        blood plasma72
         
         ↳ FP-4C4
        7211
         
        Sample 73
        blood plasma73
         
         ↳ FP-4D1
        7311
         
        Sample 74
        blood plasma74
         
         ↳ FP-4D2
        7411
         
        Sample 75
        blood plasma75
         
         ↳ FP-4D3
        7511
         
        Sample 76
        blood plasma76
         
         ↳ FP-4D4
        7611
         
        Sample 77
        blood plasma77
         
         ↳ FP-4E1
        7711
         
        Sample 78
        blood plasma78
         
         ↳ FP-4E2
        7811
         
        Sample 79
        blood plasma79
         
         ↳ FP-4E3
        7911
         
        Sample 80
        blood plasma80
         
         ↳ FP-4E4
        8011
         
        Sample 81
        blood plasma81
         
         ↳ MP-1A1
        8111
         
        Sample 82
        blood plasma82
         
         ↳ MP-1A2
        8211
         
        Sample 83
        blood plasma83
         
         ↳ MP-1A3
        8311
         
        Sample 84
        blood plasma84
         
         ↳ MP-1A4
        8411
         
        Sample 85
        blood plasma85
         
         ↳ MP-1B1
        8511
         
        Sample 86
        blood plasma86
         
         ↳ MP-1B2
        8611
         
        Sample 87
        blood plasma87
         
         ↳ MP-1B3
        8711
         
        Sample 88
        blood plasma88
         
         ↳ MP-1B4
        8811
         
        Sample 89
        blood plasma89
         
         ↳ MP-1C1
        8911
         
        Sample 90
        blood plasma90
         
         ↳ MP-1C2
        9011
         
        Sample 91
        blood plasma91
         
         ↳ MP-1C3
        9111
         
        Sample 92
        blood plasma92
         
         ↳ MP-1C4
        9211
         
        Sample 93
        blood plasma93
         
         ↳ MP-1D1
        9311
         
        Sample 94
        blood plasma94
         
         ↳ MP-1D2
        9411
         
        Sample 95
        blood plasma95
         
         ↳ MP-1D3
        9511
         
        Sample 96
        blood plasma96
         
         ↳ MP-1D4
        9611
         
        Sample 97
        blood plasma97
         
         ↳ MP-1E1
        9711
         
        Sample 98
        blood plasma98
         
         ↳ MP-1E2
        9811
         
        Sample 99
        blood plasma99
         
         ↳ MP-1E3
        9911
         
        Sample 100
        blood plasma100
         
         ↳ MP-1E4
        10011
         
        Sample 101
        blood plasma101
         
         ↳ MP-2A1
        10111
         
        Sample 102
        blood plasma102
         
         ↳ MP-2A2
        10211
         
        Sample 103
        blood plasma103
         
         ↳ MP-2A3
        10311
         
        Sample 104
        blood plasma104
         
         ↳ MP-2A4
        10411
         
        Sample 105
        blood plasma105
         
         ↳ MP-2B1
        10511
         
        Sample 106
        blood plasma106
         
         ↳ MP-2B2
        10611
         
        Sample 107
        blood plasma107
         
         ↳ MP-2B3
        10711
         
        Sample 108
        blood plasma108
         
         ↳ MP-2B4
        10811
         
        Sample 109
        blood plasma109
         
         ↳ MP-2C1
        10911
         
        Sample 110
        blood plasma110
         
         ↳ MP-2C2
        11011
         
        Sample 111
        blood plasma111
         
         ↳ MP-2C3
        11111
         
        Sample 112
        blood plasma112
         
         ↳ MP-2C4
        11211
         
        Sample 113
        blood plasma113
         
         ↳ MP-2D1
        11311
         
        Sample 114
        blood plasma114
         
         ↳ MP-2D2
        11411
         
        Sample 115
        blood plasma115
         
         ↳ MP-2D3
        11511
         
        Sample 116
        blood plasma116
         
         ↳ MP-2D4
        11611
         
        Sample 117
        blood plasma117
         
         ↳ MP-2E1
        11711
         
        Sample 118
        blood plasma118
         
         ↳ MP-2E2
        11811
         
        Sample 119
        blood plasma119
         
         ↳ MP-2E3
        11911
         
        Sample 120
        blood plasma120
         
         ↳ MP-2E4
        12011
         
        Sample 121
        blood plasma121
         
         ↳ MP-3A1
        12111
         
        Sample 122
        blood plasma122
         
         ↳ MP-3A2
        12211
         
        Sample 123
        blood plasma123
         
         ↳ MP-3A3
        12311
         
        Sample 124
        blood plasma124
         
         ↳ MP-3A4
        12411
         
        Sample 125
        blood plasma125
         
         ↳ MP-3B1
        12511
         
        Sample 126
        blood plasma126
         
         ↳ MP-3B2
        12611
         
        Sample 127
        blood plasma127
         
         ↳ MP-3B3
        12711
         
        Sample 128
        blood plasma128
         
         ↳ MP-3B4
        12811
         
        Sample 129
        blood plasma129
         
         ↳ MP-3C1
        12911
         
        Sample 130
        blood plasma130
         
         ↳ MP-3C2
        13011
         
        Sample 131
        blood plasma131
         
         ↳ MP-3C3
        13111
         
        Sample 132
        blood plasma132
         
         ↳ MP-3C4
        13211
         
        Sample 133
        blood plasma133
         
         ↳ MP-3D1
        13311
         
        Sample 134
        blood plasma134
         
         ↳ MP-3D2
        13411
         
        Sample 135
        blood plasma135
         
         ↳ MP-3D3
        13511
         
        Sample 136
        blood plasma136
         
         ↳ MP-3D4
        13611
         
        Sample 137
        blood plasma137
         
         ↳ MP-3E1
        13711
         
        Sample 138
        blood plasma138
         
         ↳ MP-3E2
        13811
         
        Sample 139
        blood plasma139
         
         ↳ MP-3E3
        13911
         
        Sample 140
        blood plasma140
         
         ↳ MP-3E4
        14011
         
        Sample 141
        blood plasma141
         
         ↳ MP-4A1
        14111
         
        Sample 142
        blood plasma142
         
         ↳ MP-4A2
        14211
         
        Sample 143
        blood plasma143
         
         ↳ MP-4A3
        14311
         
        Sample 144
        blood plasma144
         
         ↳ MP-4A4
        14411
         
        Sample 145
        blood plasma145
         
         ↳ MP-4B1
        14511
         
        Sample 146
        blood plasma146
         
         ↳ MP-4B2
        14611
         
        Sample 147
        blood plasma147
         
         ↳ MP-4B3
        14711
         
        Sample 148
        blood plasma148
         
         ↳ MP-4B4
        14811
         
        Sample 149
        blood plasma149
         
         ↳ MP-4C1
        14911
         
        Sample 150
        blood plasma150
         
         ↳ MP-4C2
        15011
         
        Sample 151
        blood plasma151
         
         ↳ MP-4C3
        15111
         
        Sample 152
        blood plasma152
         
         ↳ MP-4C4
        15211
         
        Sample 153
        blood plasma153
         
         ↳ MP-4D1
        15311
         
        Sample 154
        blood plasma154
         
         ↳ MP-4D2
        15411
         
        Sample 155
        blood plasma155
         
         ↳ MP-4D3
        15511
         
        Sample 156
        blood plasma156
         
         ↳ MP-4D4
        15611
         
        Sample 157
        blood plasma157
         
         ↳ MP-4E1
        15711
         
        Sample 158
        blood plasma158
         
         ↳ MP-4E2
        15811
         
        Sample 159
        blood plasma159
         
         ↳ MP-4E3
        15911
         
        Sample 160
        blood plasma160
         
         ↳ MP-4E4
        16011
        Expand table

        Results Overview

        Summary Table

        This table shows the summary statistics of the submitted data.
        This table shows the summary statistics of the submitted data.
        Showing 1/1 rows.
        #Peptides Quantified#Proteins Quantified
        5447
        865

        HeatMap

        This heatmap provides an overview of the performance of the quantms DIA (DIA-NN) results.
        This plot shows the pipeline performance overview. Some metrics are calculated. *Heatmap score[Contaminants]: as fraction of summed intensity with 0 = sample full of contaminants; 1 = no contaminants *Heatmap score[Pep Intensity (>23.0)]: Linear scale of the median intensity reaching the threshold, i.e. reaching 2^21 of 2^23 gives score 0.25. *Heatmap score[Charge]: Deviation of the charge 2 proportion from a representative Raw file (median). For typtic digests, peptides of charge 2 (one N-terminal and one at tryptic C-terminal R or K residue) should be dominant. Ionization issues (voltage?), in-source fragmentation, missed cleavages and buffer irregularities can cause a shift (see Bittremieux 2017, DOI: 10.1002/mas.21544) *Heatmap score[RT Alignment]: Compute 1 minus the mean absolute difference between 'RT' and 'Predicted.RT', and take the maximum of this value and 0. 1: |RT - Predicted.RT| = 0 *Heatmap score [ID rate over RT]: Judge column occupancy over retention time. Ideally, the LC gradient is chosen such that the number of identifications (here, after FDR filtering) is uniform over time, to ensure consistent instrument duty cycles. Sharp peaks and uneven distribution of identifications over time indicate potential for LC gradient optimization.Scored using 'Uniform' scoring function. i.e. constant receives good score, extreme shapes are bad *Heatmap score [Norm Factor]: Computes the mean absolute deviation (MAD) of 'Normalisation.Factor' from its mean. 0 = high variability in normalization factors; 1 = perfectly consistent normalization factors *Heatmap score [Peak Width]: Average peak width (RT.Stop - RT.Start). 1 = peak width equals 0; 0 = peak width equals 1 or greater
        Created with MultiQC

        Pipeline Result Statistics

        This plot shows the final pipeline results.
        Including Sample Name, Possible Study Variables, identified the number of peptide in the pipeline, and identified the number of modified peptide in the pipeline, eg. All data in this table are obtained from the out_msstats file. You can also remove the decoy with the `remove_decoy` parameter. In the FragPipe results summary, the data were obtained from psm.tsv.
        Showing 160/160 rows and 6/6 columns.
        Sample NameMSstats_ConditionFraction#Peptide IDs#Unambiguous Peptide IDs#Modified Peptide IDs#Protein (group) IDs
         
        Sample 1
        blood plasma
        3710
        3710
        0
        585
         
         ↳ FP-1A1
        1
        3710
        3710
        0
        585
         
        Sample 2
        blood plasma
        3856
        3856
        0
        598
         
         ↳ FP-1A2
        1
        3856
        3856
        0
        598
         
        Sample 3
        blood plasma
        3767
        3767
        0
        576
         
         ↳ FP-1A3
        1
        3767
        3767
        0
        576
         
        Sample 4
        blood plasma
        3798
        3798
        0
        579
         
         ↳ FP-1A4
        1
        3798
        3798
        0
        579
         
        Sample 5
        blood plasma
        3855
        3855
        0
        652
         
         ↳ FP-1B1
        1
        3855
        3855
        0
        652
         
        Sample 6
        blood plasma
        3921
        3921
        0
        632
         
         ↳ FP-1B2
        1
        3921
        3921
        0
        632
         
        Sample 7
        blood plasma
        3931
        3931
        0
        611
         
         ↳ FP-1B3
        1
        3931
        3931
        0
        611
         
        Sample 8
        blood plasma
        3832
        3832
        0
        585
         
         ↳ FP-1B4
        1
        3832
        3832
        0
        585
         
        Sample 9
        blood plasma
        3717
        3717
        0
        565
         
         ↳ FP-1C1
        1
        3717
        3717
        0
        565
         
        Sample 10
        blood plasma
        3706
        3706
        0
        573
         
         ↳ FP-1C2
        1
        3706
        3706
        0
        573
         
        Sample 11
        blood plasma
        3787
        3787
        0
        580
         
         ↳ FP-1C3
        1
        3787
        3787
        0
        580
         
        Sample 12
        blood plasma
        3865
        3865
        0
        582
         
         ↳ FP-1C4
        1
        3865
        3865
        0
        582
         
        Sample 13
        blood plasma
        3543
        3543
        0
        520
         
         ↳ FP-1D1
        1
        3543
        3543
        0
        520
         
        Sample 14
        blood plasma
        3867
        3867
        0
        599
         
         ↳ FP-1D2
        1
        3867
        3867
        0
        599
         
        Sample 15
        blood plasma
        3775
        3775
        0
        578
         
         ↳ FP-1D3
        1
        3775
        3775
        0
        578
         
        Sample 16
        blood plasma
        3826
        3826
        0
        583
         
         ↳ FP-1D4
        1
        3826
        3826
        0
        583
         
        Sample 17
        blood plasma
        3543
        3543
        0
        558
         
         ↳ FP-1E1
        1
        3543
        3543
        0
        558
         
        Sample 18
        blood plasma
        3653
        3653
        0
        574
         
         ↳ FP-1E2
        1
        3653
        3653
        0
        574
         
        Sample 19
        blood plasma
        3753
        3753
        0
        587
         
         ↳ FP-1E3
        1
        3753
        3753
        0
        587
         
        Sample 20
        blood plasma
        3827
        3827
        0
        601
         
         ↳ FP-1E4
        1
        3827
        3827
        0
        601
         
        Sample 21
        blood plasma
        3221
        3221
        0
        521
         
         ↳ FP-2A1
        1
        3221
        3221
        0
        521
         
        Sample 22
        blood plasma
        3326
        3326
        0
        529
         
         ↳ FP-2A2
        1
        3326
        3326
        0
        529
         
        Sample 23
        blood plasma
        3361
        3361
        0
        550
         
         ↳ FP-2A3
        1
        3361
        3361
        0
        550
         
        Sample 24
        blood plasma
        3309
        3309
        0
        523
         
         ↳ FP-2A4
        1
        3309
        3309
        0
        523
         
        Sample 25
        blood plasma
        3366
        3366
        0
        526
         
         ↳ FP-2B1
        1
        3366
        3366
        0
        526
         
        Sample 26
        blood plasma
        3278
        3278
        0
        504
         
         ↳ FP-2B2
        1
        3278
        3278
        0
        504
         
        Sample 27
        blood plasma
        3254
        3254
        0
        529
         
         ↳ FP-2B3
        1
        3254
        3254
        0
        529
         
        Sample 28
        blood plasma
        3201
        3201
        0
        495
         
         ↳ FP-2B4
        1
        3201
        3201
        0
        495
         
        Sample 29
        blood plasma
        3174
        3174
        0
        519
         
         ↳ FP-2C1
        1
        3174
        3174
        0
        519
         
        Sample 30
        blood plasma
        3358
        3358
        0
        528
         
         ↳ FP-2C2
        1
        3358
        3358
        0
        528
         
        Sample 31
        blood plasma
        3320
        3320
        0
        528
         
         ↳ FP-2C3
        1
        3320
        3320
        0
        528
         
        Sample 32
        blood plasma
        3731
        3731
        0
        589
         
         ↳ FP-2C4
        1
        3731
        3731
        0
        589
         
        Sample 33
        blood plasma
        3543
        3543
        0
        526
         
         ↳ FP-2D1
        1
        3543
        3543
        0
        526
         
        Sample 34
        blood plasma
        3539
        3539
        0
        538
         
         ↳ FP-2D2
        1
        3539
        3539
        0
        538
         
        Sample 35
        blood plasma
        3375
        3375
        0
        507
         
         ↳ FP-2D3
        1
        3375
        3375
        0
        507
         
        Sample 36
        blood plasma
        3476
        3476
        0
        531
         
         ↳ FP-2D4
        1
        3476
        3476
        0
        531
         
        Sample 37
        blood plasma
        3642
        3642
        0
        529
         
         ↳ FP-2E1
        1
        3642
        3642
        0
        529
         
        Sample 38
        blood plasma
        3635
        3635
        0
        549
         
         ↳ FP-2E2
        1
        3635
        3635
        0
        549
         
        Sample 39
        blood plasma
        3565
        3565
        0
        514
         
         ↳ FP-2E3
        1
        3565
        3565
        0
        514
         
        Sample 40
        blood plasma
        3553
        3553
        0
        529
         
         ↳ FP-2E4
        1
        3553
        3553
        0
        529
         
        Sample 41
        blood plasma
        3392
        3392
        0
        513
         
         ↳ FP-3A1
        1
        3392
        3392
        0
        513
         
        Sample 42
        blood plasma
        3548
        3548
        0
        528
         
         ↳ FP-3A2
        1
        3548
        3548
        0
        528
         
        Sample 43
        blood plasma
        3523
        3523
        0
        520
         
         ↳ FP-3A3
        1
        3523
        3523
        0
        520
         
        Sample 44
        blood plasma
        3574
        3574
        0
        523
         
         ↳ FP-3A4
        1
        3574
        3574
        0
        523
         
        Sample 45
        blood plasma
        3520
        3520
        0
        502
         
         ↳ FP-3B1
        1
        3520
        3520
        0
        502
         
        Sample 46
        blood plasma
        3464
        3464
        0
        522
         
         ↳ FP-3B2
        1
        3464
        3464
        0
        522
         
        Sample 47
        blood plasma
        3544
        3544
        0
        512
         
         ↳ FP-3B3
        1
        3544
        3544
        0
        512
         
        Sample 48
        blood plasma
        3418
        3418
        0
        499
         
         ↳ FP-3B4
        1
        3418
        3418
        0
        499
         
        Sample 49
        blood plasma
        3643
        3643
        0
        526
         
         ↳ FP-3C1
        1
        3643
        3643
        0
        526
         
        Sample 50
        blood plasma
        3496
        3496
        0
        511
         
         ↳ FP-3C2
        1
        3496
        3496
        0
        511
         
        Sample 51
        blood plasma
        3496
        3496
        0
        499
         
         ↳ FP-3C3
        1
        3496
        3496
        0
        499
         
        Sample 52
        blood plasma
        3554
        3554
        0
        505
         
         ↳ FP-3C4
        1
        3554
        3554
        0
        505
         
        Sample 53
        blood plasma
        3532
        3532
        0
        508
         
         ↳ FP-3D1
        1
        3532
        3532
        0
        508
         
        Sample 54
        blood plasma
        3588
        3588
        0
        537
         
         ↳ FP-3D2
        1
        3588
        3588
        0
        537
         
        Sample 55
        blood plasma
        3560
        3560
        0
        496
         
         ↳ FP-3D3
        1
        3560
        3560
        0
        496
         
        Sample 56
        blood plasma
        3524
        3524
        0
        507
         
         ↳ FP-3D4
        1
        3524
        3524
        0
        507
         
        Sample 57
        blood plasma
        3623
        3623
        0
        535
         
         ↳ FP-3E1
        1
        3623
        3623
        0
        535
         
        Sample 58
        blood plasma
        3727
        3727
        0
        540
         
         ↳ FP-3E2
        1
        3727
        3727
        0
        540
         
        Sample 59
        blood plasma
        3650
        3650
        0
        534
         
         ↳ FP-3E3
        1
        3650
        3650
        0
        534
         
        Sample 60
        blood plasma
        3776
        3776
        0
        548
         
         ↳ FP-3E4
        1
        3776
        3776
        0
        548
         
        Sample 61
        blood plasma
        3628
        3628
        0
        525
         
         ↳ FP-4A1
        1
        3628
        3628
        0
        525
         
        Sample 62
        blood plasma
        3557
        3557
        0
        538
         
         ↳ FP-4A2
        1
        3557
        3557
        0
        538
         
        Sample 63
        blood plasma
        3519
        3519
        0
        511
         
         ↳ FP-4A3
        1
        3519
        3519
        0
        511
         
        Sample 64
        blood plasma
        3485
        3485
        0
        520
         
         ↳ FP-4A4
        1
        3485
        3485
        0
        520
         
        Sample 65
        blood plasma
        3392
        3392
        0
        492
         
         ↳ FP-4B1
        1
        3392
        3392
        0
        492
         
        Sample 66
        blood plasma
        3567
        3567
        0
        539
         
         ↳ FP-4B2
        1
        3567
        3567
        0
        539
         
        Sample 67
        blood plasma
        3414
        3414
        0
        509
         
         ↳ FP-4B3
        1
        3414
        3414
        0
        509
         
        Sample 68
        blood plasma
        3687
        3687
        0
        546
         
         ↳ FP-4B4
        1
        3687
        3687
        0
        546
         
        Sample 69
        blood plasma
        3444
        3444
        0
        508
         
         ↳ FP-4C1
        1
        3444
        3444
        0
        508
         
        Sample 70
        blood plasma
        3357
        3357
        0
        481
         
         ↳ FP-4C2
        1
        3357
        3357
        0
        481
         
        Sample 71
        blood plasma
        3550
        3550
        0
        528
         
         ↳ FP-4C3
        1
        3550
        3550
        0
        528
         
        Sample 72
        blood plasma
        3548
        3548
        0
        528
         
         ↳ FP-4C4
        1
        3548
        3548
        0
        528
         
        Sample 73
        blood plasma
        2950
        2950
        0
        445
         
         ↳ FP-4D1
        1
        2950
        2950
        0
        445
         
        Sample 74
        blood plasma
        3547
        3547
        0
        535
         
         ↳ FP-4D2
        1
        3547
        3547
        0
        535
         
        Sample 75
        blood plasma
        3577
        3577
        0
        526
         
         ↳ FP-4D3
        1
        3577
        3577
        0
        526
         
        Sample 76
        blood plasma
        3563
        3563
        0
        522
         
         ↳ FP-4D4
        1
        3563
        3563
        0
        522
         
        Sample 77
        blood plasma
        3554
        3554
        0
        524
         
         ↳ FP-4E1
        1
        3554
        3554
        0
        524
         
        Sample 78
        blood plasma
        3462
        3462
        0
        517
         
         ↳ FP-4E2
        1
        3462
        3462
        0
        517
         
        Sample 79
        blood plasma
        3528
        3528
        0
        528
         
         ↳ FP-4E3
        1
        3528
        3528
        0
        528
         
        Sample 80
        blood plasma
        3598
        3598
        0
        520
         
         ↳ FP-4E4
        1
        3598
        3598
        0
        520
         
        Sample 81
        blood plasma
        3947
        3947
        0
        653
         
         ↳ MP-1A1
        1
        3947
        3947
        0
        653
         
        Sample 82
        blood plasma
        3619
        3619
        0
        573
         
         ↳ MP-1A2
        1
        3619
        3619
        0
        573
         
        Sample 83
        blood plasma
        3835
        3835
        0
        622
         
         ↳ MP-1A3
        1
        3835
        3835
        0
        622
         
        Sample 84
        blood plasma
        3828
        3828
        0
        584
         
         ↳ MP-1A4
        1
        3828
        3828
        0
        584
         
        Sample 85
        blood plasma
        3949
        3949
        0
        593
         
         ↳ MP-1B1
        1
        3949
        3949
        0
        593
         
        Sample 86
        blood plasma
        3759
        3759
        0
        588
         
         ↳ MP-1B2
        1
        3759
        3759
        0
        588
         
        Sample 87
        blood plasma
        3757
        3757
        0
        588
         
         ↳ MP-1B3
        1
        3757
        3757
        0
        588
         
        Sample 88
        blood plasma
        3663
        3663
        0
        583
         
         ↳ MP-1B4
        1
        3663
        3663
        0
        583
         
        Sample 89
        blood plasma
        3813
        3813
        0
        587
         
         ↳ MP-1C1
        1
        3813
        3813
        0
        587
         
        Sample 90
        blood plasma
        3846
        3846
        0
        588
         
         ↳ MP-1C2
        1
        3846
        3846
        0
        588
         
        Sample 91
        blood plasma
        3914
        3914
        0
        612
         
         ↳ MP-1C3
        1
        3914
        3914
        0
        612
         
        Sample 92
        blood plasma
        3748
        3748
        0
        574
         
         ↳ MP-1C4
        1
        3748
        3748
        0
        574
         
        Sample 93
        blood plasma
        3570
        3570
        0
        550
         
         ↳ MP-1D1
        1
        3570
        3570
        0
        550
         
        Sample 94
        blood plasma
        3788
        3788
        0
        578
         
         ↳ MP-1D2
        1
        3788
        3788
        0
        578
         
        Sample 95
        blood plasma
        3814
        3814
        0
        595
         
         ↳ MP-1D3
        1
        3814
        3814
        0
        595
         
        Sample 96
        blood plasma
        3764
        3764
        0
        580
         
         ↳ MP-1D4
        1
        3764
        3764
        0
        580
         
        Sample 97
        blood plasma
        3935
        3935
        0
        625
         
         ↳ MP-1E1
        1
        3935
        3935
        0
        625
         
        Sample 98
        blood plasma
        3692
        3692
        0
        578
         
         ↳ MP-1E2
        1
        3692
        3692
        0
        578
         
        Sample 99
        blood plasma
        3821
        3821
        0
        588
         
         ↳ MP-1E3
        1
        3821
        3821
        0
        588
         
        Sample 100
        blood plasma
        3663
        3663
        0
        589
         
         ↳ MP-1E4
        1
        3663
        3663
        0
        589
         
        Sample 101
        blood plasma
        3787
        3787
        0
        607
         
         ↳ MP-2A1
        1
        3787
        3787
        0
        607
         
        Sample 102
        blood plasma
        3789
        3789
        0
        592
         
         ↳ MP-2A2
        1
        3789
        3789
        0
        592
         
        Sample 103
        blood plasma
        3620
        3620
        0
        553
         
         ↳ MP-2A3
        1
        3620
        3620
        0
        553
         
        Sample 104
        blood plasma
        3825
        3825
        0
        605
         
         ↳ MP-2A4
        1
        3825
        3825
        0
        605
         
        Sample 105
        blood plasma
        3286
        3286
        0
        532
         
         ↳ MP-2B1
        1
        3286
        3286
        0
        532
         
        Sample 106
        blood plasma
        3194
        3194
        0
        504
         
         ↳ MP-2B2
        1
        3194
        3194
        0
        504
         
        Sample 107
        blood plasma
        3087
        3087
        0
        489
         
         ↳ MP-2B3
        1
        3087
        3087
        0
        489
         
        Sample 108
        blood plasma
        3276
        3276
        0
        528
         
         ↳ MP-2B4
        1
        3276
        3276
        0
        528
         
        Sample 109
        blood plasma
        3314
        3314
        0
        561
         
         ↳ MP-2C1
        1
        3314
        3314
        0
        561
         
        Sample 110
        blood plasma
        3134
        3134
        0
        496
         
         ↳ MP-2C2
        1
        3134
        3134
        0
        496
         
        Sample 111
        blood plasma
        3270
        3270
        0
        521
         
         ↳ MP-2C3
        1
        3270
        3270
        0
        521
         
        Sample 112
        blood plasma
        3302
        3302
        0
        529
         
         ↳ MP-2C4
        1
        3302
        3302
        0
        529
         
        Sample 113
        blood plasma
        3651
        3651
        0
        566
         
         ↳ MP-2D1
        1
        3651
        3651
        0
        566
         
        Sample 114
        blood plasma
        3815
        3815
        0
        603
         
         ↳ MP-2D2
        1
        3815
        3815
        0
        603
         
        Sample 115
        blood plasma
        3587
        3587
        0
        551
         
         ↳ MP-2D3
        1
        3587
        3587
        0
        551
         
        Sample 116
        blood plasma
        3580
        3580
        0
        539
         
         ↳ MP-2D4
        1
        3580
        3580
        0
        539
         
        Sample 117
        blood plasma
        3524
        3524
        0
        555
         
         ↳ MP-2E1
        1
        3524
        3524
        0
        555
         
        Sample 118
        blood plasma
        3335
        3335
        0
        504
         
         ↳ MP-2E2
        1
        3335
        3335
        0
        504
         
        Sample 119
        blood plasma
        3431
        3431
        0
        506
         
         ↳ MP-2E3
        1
        3431
        3431
        0
        506
         
        Sample 120
        blood plasma
        3411
        3411
        0
        497
         
         ↳ MP-2E4
        1
        3411
        3411
        0
        497
         
        Sample 121
        blood plasma
        3774
        3774
        0
        568
         
         ↳ MP-3A1
        1
        3774
        3774
        0
        568
         
        Sample 122
        blood plasma
        3728
        3728
        0
        578
         
         ↳ MP-3A2
        1
        3728
        3728
        0
        578
         
        Sample 123
        blood plasma
        3523
        3523
        0
        533
         
         ↳ MP-3A3
        1
        3523
        3523
        0
        533
         
        Sample 124
        blood plasma
        3338
        3338
        0
        506
         
         ↳ MP-3A4
        1
        3338
        3338
        0
        506
         
        Sample 125
        blood plasma
        3484
        3484
        0
        525
         
         ↳ MP-3B1
        1
        3484
        3484
        0
        525
         
        Sample 126
        blood plasma
        3381
        3381
        0
        498
         
         ↳ MP-3B2
        1
        3381
        3381
        0
        498
         
        Sample 127
        blood plasma
        3486
        3486
        0
        533
         
         ↳ MP-3B3
        1
        3486
        3486
        0
        533
         
        Sample 128
        blood plasma
        3159
        3159
        0
        488
         
         ↳ MP-3B4
        1
        3159
        3159
        0
        488
         
        Sample 129
        blood plasma
        3556
        3556
        0
        510
         
         ↳ MP-3C1
        1
        3556
        3556
        0
        510
         
        Sample 130
        blood plasma
        3531
        3531
        0
        508
         
         ↳ MP-3C2
        1
        3531
        3531
        0
        508
         
        Sample 131
        blood plasma
        3567
        3567
        0
        510
         
         ↳ MP-3C3
        1
        3567
        3567
        0
        510
         
        Sample 132
        blood plasma
        3556
        3556
        0
        511
         
         ↳ MP-3C4
        1
        3556
        3556
        0
        511
         
        Sample 133
        blood plasma
        3708
        3708
        0
        547
         
         ↳ MP-3D1
        1
        3708
        3708
        0
        547
         
        Sample 134
        blood plasma
        3486
        3486
        0
        502
         
         ↳ MP-3D2
        1
        3486
        3486
        0
        502
         
        Sample 135
        blood plasma
        3545
        3545
        0
        513
         
         ↳ MP-3D3
        1
        3545
        3545
        0
        513
         
        Sample 136
        blood plasma
        3608
        3608
        0
        526
         
         ↳ MP-3D4
        1
        3608
        3608
        0
        526
         
        Sample 137
        blood plasma
        3715
        3715
        0
        545
         
         ↳ MP-3E1
        1
        3715
        3715
        0
        545
         
        Sample 138
        blood plasma
        3654
        3654
        0
        536
         
         ↳ MP-3E2
        1
        3654
        3654
        0
        536
         
        Sample 139
        blood plasma
        3569
        3569
        0
        520
         
         ↳ MP-3E3
        1
        3569
        3569
        0
        520
         
        Sample 140
        blood plasma
        3514
        3514
        0
        511
         
         ↳ MP-3E4
        1
        3514
        3514
        0
        511
         
        Sample 141
        blood plasma
        546
        546
        0
        136
         
         ↳ MP-4A1
        1
        546
        546
        0
        136
         
        Sample 142
        blood plasma
        3609
        3609
        0
        542
         
         ↳ MP-4A2
        1
        3609
        3609
        0
        542
         
        Sample 143
        blood plasma
        3579
        3579
        0
        528
         
         ↳ MP-4A3
        1
        3579
        3579
        0
        528
         
        Sample 144
        blood plasma
        3554
        3554
        0
        513
         
         ↳ MP-4A4
        1
        3554
        3554
        0
        513
         
        Sample 145
        blood plasma
        3562
        3562
        0
        540
         
         ↳ MP-4B1
        1
        3562
        3562
        0
        540
         
        Sample 146
        blood plasma
        3553
        3553
        0
        503
         
         ↳ MP-4B2
        1
        3553
        3553
        0
        503
         
        Sample 147
        blood plasma
        3440
        3440
        0
        503
         
         ↳ MP-4B3
        1
        3440
        3440
        0
        503
         
        Sample 148
        blood plasma
        3460
        3460
        0
        505
         
         ↳ MP-4B4
        1
        3460
        3460
        0
        505
         
        Sample 149
        blood plasma
        3659
        3659
        0
        555
         
         ↳ MP-4C1
        1
        3659
        3659
        0
        555
         
        Sample 150
        blood plasma
        3437
        3437
        0
        524
         
         ↳ MP-4C2
        1
        3437
        3437
        0
        524
         
        Sample 151
        blood plasma
        3484
        3484
        0
        542
         
         ↳ MP-4C3
        1
        3484
        3484
        0
        542
         
        Sample 152
        blood plasma
        3348
        3348
        0
        524
         
         ↳ MP-4C4
        1
        3348
        3348
        0
        524
         
        Sample 153
        blood plasma
        3669
        3669
        0
        536
         
         ↳ MP-4D1
        1
        3669
        3669
        0
        536
         
        Sample 154
        blood plasma
        3552
        3552
        0
        506
         
         ↳ MP-4D2
        1
        3552
        3552
        0
        506
         
        Sample 155
        blood plasma
        3506
        3506
        0
        542
         
         ↳ MP-4D3
        1
        3506
        3506
        0
        542
         
        Sample 156
        blood plasma
        2876
        2876
        0
        449
         
         ↳ MP-4D4
        1
        2876
        2876
        0
        449
         
        Sample 157
        blood plasma
        3342
        3342
        0
        515
         
         ↳ MP-4E1
        1
        3342
        3342
        0
        515
         
        Sample 158
        blood plasma
        3450
        3450
        0
        514
         
         ↳ MP-4E2
        1
        3450
        3450
        0
        514
         
        Sample 159
        blood plasma
        3640
        3640
        0
        534
         
         ↳ MP-4E3
        1
        3640
        3640
        0
        534
         
        Sample 160
        blood plasma
        3585
        3585
        0
        540
         
         ↳ MP-4E4
        1
        3585
        3585
        0
        540
        Expand table

        Identification Summary

        Number of Peptides identified Per Protein

        This plot shows the number of peptides per protein in quantms pipeline final result
        This statistic is extracted from the out_msstats file. Proteins supported by more peptide identifications can constitute more confident results.
        Created with MultiQC

        ProteinGroups Count

        Number of protein groups per raw file.
        Based on statistics calculated from mzTab, mzIdentML (mzid), DIA-NN report files, or FragPipe psm.tsv.
        Created with MultiQC

        Peptide ID Count

        Number of unique (i.e. not counted twice) peptide sequences including modifications per Raw file.
        Based on statistics calculated from mzTab, mzIdentML (mzid), DIA-NN report files, or FragPipe psm.tsv.
        Created with MultiQC

        Peptide Length Distribution

        Peptide length distribution per Run.
        Peptide length distribution.
        FragPipe: psm.tsv ('Peptide Length': number of residues in the peptide sequence).
        MaxQuant: evidence.txt ('Length': the length of the sequence stored in the column 'Sequence').
        DIA-NN: report.tsv (the length of the 'Stripped.Sequence').
        quantms: *.mzTab (the length of sequence).
        Created with MultiQC

        Quantification Analysis

        Peptides Quantification Table

        This plot shows the quantification information of peptides in the final result (mainly the mzTab file).
        The quantification information of peptides is obtained from the MSstats input file. The table shows the quantitative level and distribution of peptides in different study variables, run and peptiforms. The distribution show all the intensity values in a bar plot above and below the average intensity for all the fractions, runs and peptiforms. * BestSearchScore: It is equal to 1 - min(Q.Value) for DIA datasets. Then it is equal to 1 - min(best_search_engine_score[1]), which is from best_search_engine_score[1] column in mzTab peptide table for DDA datasets. * Average Intensity: Average intensity of each peptide sequence across all conditions with NA=0 or NA ignored. * Peptide intensity in each condition (Eg. `CT=Mixture;CN=UPS1;QY=0.1fmol`): Summarize intensity of fractions, and then mean intensity in technical replicates/biological replicates separately.
        Showing 50/50 rows and 5/5 columns.
        PeptideIDProtein NamePeptide SequenceBest Search ScoreAverage Intensityblood plasma
        1
        IPSP_HUMAN
        AAAATGTLFTFR
        1.0000
        7.2108
        7.2108
        2
        TFR1_HUMAN
        AAAEVAGQFVLK
        1.0000
        6.2663
        6.2663
        3
        TLN1_HUMAN
        AAAFEEQENETVVVK
        0.9928
        6.6869
        6.6869
        4
        AOC3_HUMAN
        AAALAHLDR
        1.0000
        5.5533
        5.5533
        5
        POSTN_HUMAN
        AAALTSDLLEALGR
        1.0000
        6.0312
        6.0312
        6
        ANAG_HUMAN
        AAAVSEAEADFYEQNSR
        1.0000
        5.0776
        5.0776
        7
        TTHY_HUMAN
        AADDTWEPFASGK
        1.0000
        9.7129
        9.7129
        8
        FA5_HUMAN
        AADLEQQAVFAVFDENK
        1.0000
        7.1805
        7.1805
        9
        PHB1_HUMAN
        AAELLANSLATAGDGLLELR
        1.0000
        5.8910
        5.8910
        10
        1433E_HUMAN
        AAFDDALAELDTLSEESYK
        1.0000
        5.6967
        5.6967
        11
        COMD3_HUMAN
        AAFQSLLDAQADEAVLDHPDLK
        0.9959
        6.9196
        6.9196
        12
        PTPRF_HUMAN
        AAGTEGPFQEVDGVATTR
        1.0000
        5.8582
        5.8582
        13
        NCAM1_HUMAN
        AAHFVFR
        0.9997
        6.0236
        6.0236
        14
        APOB_HUMAN
        AALGKLPQQANDYLNSFNWER
        1.0000
        8.2900
        8.2900
        15
        ACE_HUMAN
        AALPAQELEEYNK
        1.0000
        5.6296
        5.6296
        16
        LRP1_HUMAN
        AALSGANVLTLLEK
        1.0000
        5.7929
        5.7929
        17
        ITIH1_HUMAN
        AALSGENAGLVR
        1.0000
        9.1727
        9.1727
        18
        APOB_HUMAN
        AALTELSLGSAYQAMLLGVDSK
        1.0000
        7.5942
        7.5942
        19
        ANGT_HUMAN
        AAMVGMLANFLGFR
        1.0000
        6.5836
        6.5836
        20
        HYOU1_HUMAN
        AANSLEAFLFETQDK
        1.0000
        6.3650
        6.3650
        21
        COR1A_HUMAN
        AAPEASGTPSSDAVSR
        1.0000
        4.9994
        4.9994
        22
        QSOX1_HUMAN
        AAPGQEPPEHMAELQR
        1.0000
        6.9875
        6.9875
        23
        CO6A3_HUMAN
        AAPLQGMLPGLLAPLR
        1.0000
        5.4851
        5.4851
        24
        IGLC7_HUMAN
        AAPSVTLFPPSSEELQANK
        1.0000
        8.2159
        8.2159
        25
        LCAT_HUMAN
        AAPYDWR
        0.9997
        7.1839
        7.1839
        26
        FCG2A_HUMAN
        AAQFEPPGR
        1.0000
        6.2442
        6.2442
        27
        A2MG_HUMAN
        AAQVTLQSSGTFSSK
        1.0000
        7.2145
        7.2145
        28
        CO7_HUMAN
        AASGTQNNVLR
        1.0000
        6.1424
        6.1424
        29
        APOB_HUMAN
        AASGTTGTYQEWK
        1.0000
        8.5080
        8.5080
        30
        APOB_HUMAN
        AASGTTGTYQEWKDK
        1.0000
        6.8078
        6.8078
        31
        PHB1_HUMAN
        AATFGLLLDDVSLTHLTFGK
        0.9989
        6.5604
        6.5604
        32
        APOE_HUMAN
        AATVGSLAGQPLQER
        1.0000
        8.5561
        8.5561
        33
        HEM2_HUMAN
        AAVLEAMTAFR
        1.0000
        5.8607
        5.8607
        34
        ENOA_HUMAN
        AAVPSGASTGLYEALELR
        1.0000
        6.5722
        6.5722
        35
        CO3_HUMAN
        AAVYHHFLSDGVR
        1.0000
        9.3946
        9.3946
        36
        CO3_HUMAN
        AAVYHHFLSDGVRK
        1.0000
        7.6217
        7.6217
        37
        CONTAM_HBA_HUMAN;HBA_HUMAN
        AAWGKVGAHAGEYGAEALER
        1.0000
        6.7950
        6.7950
        38
        ALDOA_HUMAN
        ADDGRPFPQVLK
        1.0000
        6.6966
        6.6966
        39
        ALBU_HUMAN;CONTAM_ALBU_HUMAN
        ADDKETCFAEEGK
        1.0000
        6.8517
        6.8517
        40
        CONTAM_PRDX1_HUMAN;PRDX1_HUMAN
        ADEGLSFR
        0.9948
        5.8632
        5.8632
        41
        PCSK9_HUMAN
        ADEYQPPDGGSLVEVYLLDTSLQSDHRELEGR
        1.0000
        5.3807
        5.3807
        42
        B3AT_HUMAN
        ADFLEQPVLGFVR
        1.0000
        6.2023
        6.2023
        43
        CAH1_HUMAN;CONTAM_CAH1_HUMAN
        ADGLAVLGVLMK
        1.0000
        7.6744
        7.6744
        44
        CD109_HUMAN
        ADGNQLTLEER
        1.0000
        5.8432
        5.8432
        45
        CO4B_HUMAN
        ADGSYAAWLSR
        1.0000
        8.7034
        8.7034
        46
        ASGR2_HUMAN
        ADHDALLFHLK
        1.0000
        5.8520
        5.8520
        47
        BGH3_HUMAN
        ADHHATNGVVHLLDK
        1.0000
        6.6119
        6.6119
        48
        FA5_HUMAN
        ADKPLSLHPQGLR
        1.0000
        6.7216
        6.7216
        49
        CONTAM_K1C17_HUMAN;K1C17_HUMAN
        ADLEMQLENLK
        0.9932
        6.9798
        6.9798
        50
        CONTAM_K1C14_HUMAN;K1C14_HUMAN
        ADLEMQLESLKEELAYLK
        1.0000
        6.6003
        6.6003
        Expand table

        Protein Quantification Table

        This plot shows the quantification information of proteins in the final result (mainly the mzTab file).
        The quantification information of proteins is obtained from the msstats input file. The table shows the quantitative level and distribution of proteins in different study variables and run. * Peptides_Number: The number of peptides for each protein. * Average Intensity: Average intensity of each protein across all conditions with NA=0 or NA ignored. * Protein intensity in each condition (Eg. `CT=Mixture;CN=UPS1;QY=0.1fmol`): Summarize intensity of peptides.
        Showing 50/50 rows and 4/4 columns.
        ProteinIDProtein NameNumber of PeptidesAverage Intensityblood plasma
        1
        1433B_HUMAN
        1
        5.5428
        5.5428
        2
        1433E_HUMAN
        6
        7.0074
        7.0074
        3
        1433T_HUMAN
        1
        5.3322
        5.3322
        4
        1433Z_HUMAN
        5
        7.0499
        7.0499
        5
        4F2_HUMAN
        8
        7.2806
        7.2806
        6
        6PGD_HUMAN
        2
        6.0220
        6.0220
        7
        A1AG1_HUMAN
        10
        8.4759
        8.4759
        8
        A1AG2_HUMAN
        6
        8.6081
        8.6081
        9
        A1AT_HUMAN
        36
        10.3121
        10.3121
        10
        A1BG_HUMAN
        14
        10.0529
        10.0529
        11
        A2AP_HUMAN
        15
        9.5034
        9.5034
        12
        A2GL_HUMAN
        10
        9.3554
        9.3554
        13
        A2MG_HUMAN
        63
        9.5265
        9.5265
        14
        A4_HUMAN
        1
        5.6606
        5.6606
        15
        AACT_HUMAN
        28
        10.3909
        10.3909
        16
        AATC_HUMAN
        2
        5.4660
        5.4660
        17
        ABCD3_HUMAN
        1
        6.0229
        6.0229
        18
        ACADV_HUMAN
        1
        7.3439
        7.3439
        19
        ACES_HUMAN
        1
        5.3543
        5.3543
        20
        ACE_HUMAN
        8
        7.7527
        7.7527
        21
        ACTBL_HUMAN
        6
        7.8915
        7.8915
        22
        ACTB_HUMAN;ACTG_HUMAN
        8
        8.4190
        8.4190
        23
        ACTC_HUMAN
        1
        5.8513
        5.8513
        24
        ACTN1_HUMAN
        19
        7.6279
        7.6279
        25
        ACTS_HUMAN
        9
        8.1438
        8.1438
        26
        ADA2_HUMAN
        5
        6.8083
        6.8083
        27
        ADEC1_HUMAN
        1
        5.4188
        5.4188
        28
        ADIPO_HUMAN
        5
        7.9267
        7.9267
        29
        ADT2_HUMAN
        2
        6.8402
        6.8402
        30
        ADT3_HUMAN
        1
        5.8031
        5.8031
        31
        AFAM_HUMAN
        22
        9.7319
        9.7319
        32
        AGRE1_HUMAN
        1
        6.1030
        6.1030
        33
        AGRF5_HUMAN
        3
        6.5983
        6.5983
        34
        AGRG6_HUMAN
        3
        6.3593
        6.3593
        35
        AGRL4_HUMAN
        2
        5.5922
        5.5922
        36
        AHSP_HUMAN
        2
        6.2100
        6.2100
        37
        AL1A1_HUMAN
        4
        6.3021
        6.3021
        38
        AL4A1_HUMAN
        1
        6.4031
        6.4031
        39
        ALBU_HUMAN;CONTAM_ALBU_HUMAN
        46
        10.8600
        10.8600
        40
        ALDOA_HUMAN
        8
        7.6226
        7.6226
        41
        ALDOB_HUMAN
        8
        7.7182
        7.7182
        42
        ALS_HUMAN
        22
        9.2564
        9.2564
        43
        AMBP_HUMAN
        9
        9.1926
        9.1926
        44
        AMD_HUMAN
        4
        5.9594
        5.9594
        45
        AMPE_HUMAN
        4
        6.6902
        6.6902
        46
        AMPN_HUMAN
        24
        7.9286
        7.9286
        47
        AMY1A_HUMAN;AMY1B_HUMAN;AMY1C_HUMAN
        1
        4.5475
        4.5475
        48
        AMYP_HUMAN
        6
        6.3282
        6.3282
        49
        ANAG_HUMAN
        9
        7.0657
        7.0657
        50
        ANGI_HUMAN
        3
        6.9475
        6.9475
        Expand table

        Intensity Distribution

        log2(Precursor.Quantity) for each Run (or Sample).
        [DIA-NN: main report] log2(Precursor.Quantity) for each Run (or Sample).

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Standard Deviation of Intensity

        Standard deviation of intensity by sample (experimental conditions).
        [DIA-NN: report.tsv] Sample grouping is derived from the SDRF when available; otherwise, it is parsed from "Run" names. First, identify the experimental conditions from the "Run" name. Then, group the data by experimental condition and Modified.Sequence, and calculate the standard deviation of log2(Precursor.Quantity).

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        MS1 Analysis

        MS1 Area Distribution

        log2(Ms1.Area) for each Run.
        [DIA-NN: report.tsv] log2(Ms1.Area) for each Run. Ms1.Area: non-normalised MS1 peak area.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        MS2 and Spectral Stats

        Distribution of Precursor Charges

        This is a bar chart representing the distribution of the precursor ion charges for a given whole experiment.
        [DIA-NN: main report] distribution of the precursor ion charges for a given whole experiment. Precursor.Charge: the charge of the precursor.
        Created with MultiQC

        Charge-state

        The distribution of the charge-state of the precursor ion.
        [DIA-NN: main report] The distribution of the charge-state of the precursor ion (Precursor.Charge).
        Created with MultiQC

        RT Quality Control

        IDs over RT

        Distribution of retention time, derived from the main report.
        [DIA-NN: main report] Distribution of retention time (RT) for each run.

        This plot allows to judge column occupancy over retention time. Ideally, the LC gradient is chosen such that the number of identifications (here, after FDR filtering) is uniform over time, to ensure consistent instrument duty cycles. Sharp peaks and uneven distribution of identifications over time indicate potential for LC gradient optimization. See [Moruz 2014, DOI: 10.1002/pmic.201400036](https://pubmed.ncbi.nlm.nih.gov/24700534/) for details.

        Created with MultiQC

        Normalisation Factor over RT

        Distribution of Normalisation.Factor with retention time, derived from the main report.
        [DIA-NN: main report] Distribution of Normalisation.Factor with retention time (RT) for each run. RT: the retention time (RT) of the PSM in minutes. Normalisation.Factor: normalisation factor applied to the precursor in the specific run, i.e. normalised quantity = normalisation factor X non-normalised quantity
        Created with MultiQC

        FWHM over RT

        Distribution of FWHM with retention time, derived from the main report. FWHM: estimated peak width at half-maximum.
        [DIA-NN: main report] Distribution of FWHM with retention time (RT) for each run. RT: the retention time (RT) of the PSM in minutes. FWHM: estimated peak width at half-maximum; note that the accuracy of such estimates sometimes strongly depends on the DIA cycle time and sample injection amount, i.e. they can only be used to evaluate chromatographic performance in direct comparisons with similar settings, including the scan window; another caveat is that FWHM does not reflect any peak tailing.
        Created with MultiQC

        Peak Width over RT

        Distribution of peak width with retention time, derived from the main report. Peak Width = RT.Stop - RT.Start.
        [DIA-NN: main report] Distribution of peak width with retention time (RT) for each run. RT: the retention time (RT) of the PSM in minutes. RT.Start and RT.Stop: peak boundaries.
        Created with MultiQC

        Absolute RT Error over RT

        Distribution of rt error with retention time, derived from the main report.
        [DIA-NN: main report] Distribution of absolute RT error (|RT - Predicted.RT|) with retention time (RT) for each run. RT: the retention time (RT) of the PSM in minutes. Predicted.RT: predicted RT based on the iRT.
        Created with MultiQC

        LOESS RT ~ iRT

        Distribution of LOESS RT ~ iRT for each run, derived from the main report.
        [DIA-NN: main report] Distribution of LOESS RT ~ iRT for each run. RT: the retention time (RT) of the PSM in minutes. iRT: reference RT as recorded in the spectral library.
        Created with MultiQC